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A Primer on Soil Microbes – An Interview with Sarah Hargreaves

Most of us who work in prairies think mostly about what we see aboveground. I guess that’s understandable, but to ignore the complex and critical functioning of the soil and its inhabitants is to ignore much of what really drives grassland ecology. Of course if we DID want to focus belowground, what would we actually focus on? How much do you know about soil fungi or bacteria?

Exactly. Me too.

This is why I was excited that Sarah Hargreaves agreed to an interview about the mysterious world of soil microbes. Sarah is finishing up her PhD in microbial ecology at Iowa State University. That means she’s not only up to speed on what’s known about soil microbes in the scientific literature, she’s also been studying them herself for the last several years. A perfect person to throw hard questions at.

What do you know the little creatures that live belowground in prairies? And no, prairie dogs don’t count.

So, here are my initial questions for Sarah, followed by her answers. As you’ll see, she’s an excellent writer, and can communicate complex ideas in a very accessible way. Because of that, I’ve also asked her if she’d be willing to answer follow up questions from both me and you – and she agreed (though she asked if she could wait until she finishes her dissertation, which I think is due TODAY!)

So, after you read this post, leave any questions you have in the comments section, and we’ll see if Sarah can answer a few of them in a future post.

What is a soil microbe? What broad taxa are we really talking about?

Soil microbes span all three domains of life and include bacteria, archaea, fungi. They are the most diverse group of organisms, comprising the vast majority of living organisms on earth! Bacterial and archaea are single-celled and not visible to the naked eye unless clumped together in biofilms. Although bacteria and archaea are similar in many ways, archaea often live in extreme environments, like hot springs or salt lakes, and perform more obscure functions, like transforming methane. Fungi, in contrast, are multicellular organisms. Because of the visible fruiting bodies (“mushrooms”) of some fungi, it may seem odd that they are “microorganisms”. The vast majority of a soil fungus, however, lives below the soil surface in the form of mycelia, which consist of root-like structures called hyphae.

Now and then we get a look at soil fungi, but only when they pop up above ground.

What roles do microbes play in prairie soils?

By releasing digestive enzymes into the soil environment, microbes break down dead plants, animals, and other microbes. This process of recycling makes nutrients available to living plants, soil microfauna and microbes. Decomposition by microbes also builds soil organic matter, which gives prairie soil its beautiful dark color, provides rich texture, and stores nutrients, carbon, and water. All of these factors combine to create a healthy environment for the web of life to thrive: for plants to grow, soil microfauna to explore, and animals to burrow. Soil microbes are also important partners to plants. In exchange for carbon from the plant, symbiotic bacteria (e.g. nitrogen fixers associated with legumes) and fungi (i.e. mycorrhizae associated with prairie plants) greatly enhance plant nutrient uptake.

Is it fair to compare our ability to describe the world of soil microbes to looking into a room through the keyhole?

Microbes are the most diverse type of organism on earth and soil is arguably the most complex matrix, so for microbes, it’s more like looking into a room through a pinhole – this means the field of soil microbiology is a very exciting place to be! While we have cultured (grown) some microbes in the laboratory for over a century, soil microbiology was previously limited by our ability to isolate and cultivate the vast majority of them. Largely as a result of the human genome and human microbiome projects, new sequencing technologies now make it possible to sequence the immense diversity of the soil microbiome directly from DNA extracted from soil. From these studies, we have learned that microbes are far more diverse and ecologically important than we previously thought. Sequencing has also put pressure on culturing techniques, and we are becoming much better at growing microbes in the lab. My hope is that future advances in soil microbiology will couple sequencing with culturing in order to understand the ecology of specific microbes and identify keystone microbes that can be targeted in restoration.

What else would you want someone interested in prairie ecology to understand or think about in terms of soil microbes?

Microorganisms, and microbial communities, are not all equal. For example, fungal-to-bacterial ratios are critical to soil health and sustainability. This is because soils with more fungi relative to bacteria (higher fungal to bacterial ratios) regain structure faster, retain more nitrogen and are more resilient to drought and floods. In addition, all bacterial and fungi aren’t equal. Ideally, a prairie soil has a mix of fast and slow growing bacteria and a diversity of symbiotic fungi so that prairie plants can find an ideal match. Finally, while microbes are the foundation of a healthy soil, they are part of a larger soil food web that must be intact in order to sustain the microbial community.

As prairie managers and ecologists, we think a lot about the relative abundance of plants, but not necessarily fungi or bacteria…

So, is there an optimal ratio of fungi to bacteria in soils?

“Healthier” soils generally have a fungal-dominated community. Given variability in the measurements we use and differences across sites, it is hard to pinpoint an optimal ratio; it is fairer to say that the ratio should increase with restoration.

The fungal to bacterial ratio is important because of the different lifestyles of bacteria and fungi. Bacteria have faster turnover rates (i.e. short life cycles), such that bacterial-dominated communities are linked to faster rates of nitrogen cycling and subsequent N losses from soil. In contrast, fungi have slower life cycles, which result in greater retention of nitrogen in the soil. Due to their extensive hyphal networks, fungi are also thought to be larger contributors to both the production of enzymes involved in decomposition and aggregate formation, and resistant to drought. On a community-level, fungal hyphae are the “internet of the soil” – they facilitate connections among other microbes and plants, helping plants to acquire nutrients and alleviate plant water stress. This doesn’t mean bacteria aren’t good! It is the balance between bacteria and fungi that seems to be most important.

What’s known about how prairie restoration and management can impact soil microbial communities?

First, diversity begets diversity, so it’s important to start with a diverse mixture of native prairie plants. There is also some evidence to show that prairie burns help maintain
a good fungal to bacterial ratio by promoting fungal abundance.

However, while we know some groups of microbes are very important in prairie soils – like Verrucomicrobia bacteria that dominate native prairie soils and arbuscular mycorrhizal fungi that form symbiotic relationships with plants – there is still a lot of work to be done to understand how to manage restoration for these and other specific groups of microbes. Even more, past land use has a legacy that will determine what might be needed to restore a rich diversity of soil microbes. Nitrogen fertilization, pesticides and tillage can all have lasting impacts on the types of organisms that are active in a soil. That said, the microbes are there, often in a dormant state, so they do have the capacity to come back and improve soil health when and if the conditions are right.

When we convert cropland to prairie, we just broadcast seeds on top of the ground, but what’s belowground has a huge impact on what kind of plant community is formed.

There is certainly lots to learn… Speaking of that, what story is emerging from your particular research on soil microbes in agricultural systems?

My graduate research contrasts soil microbial communities in conventional corn-based agricultural systems with alternative agricultural systems that incorporate perennial plants. The idea is that, by providing microbes with perennial root systems, they have a richer “buffet” of food that they can use to restore soil health. What I am finding is that newly established perennial cropping systems improve the function of the microbial communities but I have not yet seen dramatic changes in the diversity of the microbial communities. The perennial cropping system that I work with is a switchgrass monoculture and my results are mirrored by work in a diverse prairie cropping system. Overall, these results tell me that perennial plants in agricultural ecosystems can restore soil microbes, but practices such as fertilization and harvesting likely limit the rate and extent of restoration.

(THANK YOU to Sarah for taking time away from her dissertation writing to help us understand more about soil microbes!)

About Chris Helzer

Chris Helzer is the Director of Science for The Nature Conservancy in Nebraska. His main role is to evaluate and capture lessons from the Conservancy’s land management and restoration work and then share those lessons with other landowners – both private and public. In addition, Chris works to raise awareness about the importance of prairies and their conservation through his writing, photography, and presentations to various groups.
Chris is also the author of "The Ecology and Management of Prairies in the Central United States", published by the University of Iowa Press. He lives in Aurora, Nebraska with his wife Kim and their children.

I serve as a mentor for students at a nationally known magnet school who need help with science fair projects. Would you be able to make some suggestions to me for potential projects in this area? It looks like a fertile area for research!

Thanks for this great primer! Sarah, what are the things land managers should be doing right now to help advance research in this critical field of studies? I was brought up on the “collect as much data as you can” school of thought and we have planned some restoration projects (mostly replacing exotic KR bluestem) – I’d love to know what I should be doing before we begin our restoration projects to best track progress in microbes as we reestablish native grasses. Is this as simple as just taking soil samples?
(Rachael Ranft, The Nature Conservancy in Central Texas)

I have thought several times about the possibility of transplanting small amounts of soil (say, a few 5-gallon buckets worth) from a remnant prairie into a prairie restoration to help re-diversify the soil organisms in these ecological restorations. What are your thoughts on this? Would it be too little soil to make a difference? Would the soil microbes be too specialized to grow and thrive in a different soil environment?

This paper might be helpful: http://onlinelibrary.wiley.com/doi/10.1111/j.1526-100X.2010.00752.x/full
Many of the micro-organisms that are likely to improve restoration outcomes (e.g. mycorrhizae) depend on plants. So, how you introduce those microbes to a restoration will matter. The paper I linked to inoculated “nurse plants” and raised these seedlings before transplanting them, along with at least some components of the soil community. There’s lots of work left to do, but this approach seems really promising. It also doesn’t require a lot of soil, so damage to remnants can be minimal.

I have not been interested in prairie ecology for that long but I have had previous endeavors in the botanical field that have brought the soil food web to my attention. So thank you Sarah for the excellent responses and thank you Chris, for bringing this interview to us!

I’m curious about the bacterial to fungal ratios across prairie moisture gradients…is the ratio relatively constant between wet prairie, mesic, and xeric sites? In dry landscapes, we hear about cryptogamic crusts, which I understand are mainly formed by Cyanobacteria. What do we know about the interrelationships between the bacteria and other organisms in these crusts, and how to establish them in arid disturbed sites?

Sarah/Chris- Thanks so much for this little known aspect of prairie ecology! Related to Danelle’s question about transplanting small amounts of soil from an existing prairie to a new restoration to “seed” the mycorrhizzae: I have tried taking 4-6 in/10-15 cm long soil cores with a soil sampler from an existing prairie & interred these randomly into new plantings. I have no idea whether they worked or not, but it did make me feel good! Can this work, and if so, how best is this done? Do some non-native species have the ability to “prep” the soil with mycorrhizzae? I am thinking of species like Kentucky Bluegrass & Smooth Brome, which often dominate areas before we nuke them & go in to attempt to restore the area. Sometimes these areas restore easier than cultivated croplands. I’ve always thought that may be due to the presence of at least some microflora in these non-native grasslands. Can you make your own mycorrhizal extract, or are commercially- available, non-specific ones worthwhile to add to a restoration? Thanks!!

It’s in the soil! This is the phrase I often hear from botanists and ecologists to explain abrupt differences or changes in plant community composition when all other environmental conditions appear similar. An example of these abrupt differences in plant communities is the adjoining boundary of a planted prairie to a remnant prairie even when the planted species are closely matched to the remnant species. These boundaries are visible for decades. Another is a very distinct “vegetated wall” where an invasive species, that has consumed other areas of the prairie, just can’t seem to penetrate. So, is it in the soil? Can soil distribution of microbes be very abrupt in composition? Thanks, David

What an interesting post! I’m especially interested in the comment that ‘prairie burns help maintain a good fungal to bacterial ratio by promoting fungal abundance’. Can you explain how prairie burns help promote fungi? And thsi second question may not really fit in the scope of these discussions, but I’ll ask it anyway: In the case of areas where there has been concentrated animal urea and feced laid down for a long time (farm barnyards, feedlots, etc.) often there are almost monocultures of plants such as hemlock. Is it likely that the normal diversity of soil microbes have been destroyed in those kinds of places, or just dormant, and what (if anything) could be done to return those soils to ‘health’, beyond simply removing the soil and spreading it out over other areas.

My two questions follow. How quickly do soil organisms expand into former cropland habitat? Has there been any study that compares an effort to develop the soil microbial community before the start of ecological restoration with a control?